AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa1223310

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa1223310 MtrunA17_Chr4g0074791 85.526 76 11 0 1 76 354 429 1.72e-37 131
Msa1223310 MtrunA17_Chr4g0074811 71.429 91 25 1 1 90 349 439 5.89e-35 124
Msa1223310 MtrunA17_Chr1g0157131 63.736 91 32 1 1 90 332 422 3.30e-31 114
Msa1223310 MtrunA17_Chr5g0444171 58.242 91 37 1 1 90 350 440 1.48e-28 106
Msa1223310 MtrunA17_Chr3g0098951 62.637 91 32 2 1 90 342 431 2.35e-28 106
Msa1223310 MtrunA17_Chr8g0387671 58.242 91 37 1 1 90 324 414 1.94e-26 100
Msa1223310 MtrunA17_Chr5g0397101 57.647 85 35 1 7 90 330 414 4.41e-25 97.1
Msa1223310 MtrunA17_Chr0c02g0489761 54.945 91 40 1 1 90 336 426 7.27e-24 93.6
Msa1223310 MtrunA17_Chr5g0441691 52.747 91 42 1 1 90 326 416 1.57e-23 92.8
Msa1223310 MtrunA17_Chr8g0385341 55.294 85 37 1 7 90 294 378 3.04e-22 89.0
Msa1223310 MtrunA17_Chr3g0131181 55.294 85 37 1 7 90 293 377 4.19e-22 88.6
Msa1223310 MtrunA17_Chr1g0176751 55.294 85 37 1 7 90 388 472 1.44e-21 87.0
Msa1223310 MtrunA17_Chr1g0176421 51.136 88 42 1 4 90 422 509 4.26e-21 85.9
Msa1223310 MtrunA17_Chr1g0200601 49.438 89 44 1 3 90 290 378 3.57e-20 83.2
Msa1223310 MtrunA17_Chr5g0448721 48.889 90 42 2 5 90 355 444 8.66e-20 82.0
Msa1223310 MtrunA17_Chr1g0170281 50.588 85 41 1 7 90 382 466 2.47e-19 80.9
Msa1223310 MtrunA17_Chr7g0267751 47.191 89 45 2 3 90 396 483 2.87e-19 80.5
Msa1223310 MtrunA17_Chr4g0059951 44.444 81 44 1 1 80 331 411 9.13e-16 70.5
Msa1223310 MtrunA17_Chr7g0242561 37.363 91 56 1 1 90 314 404 1.41e-13 64.3
Msa1223310 MtrunA17_Chr4g0033371 44.615 65 35 1 14 77 343 407 9.66e-12 59.3
Msa1223310 MtrunA17_Chr7g0257751 40.789 76 44 1 16 90 331 406 1.25e-11 58.9
Msa1223310 MtrunA17_Chr5g0405421 38.667 75 45 1 1 74 359 433 3.03e-11 57.8
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa1223310 AT3G20410.2 62.637 91 33 1 1 90 349 439 1.69e-29 109
Msa1223310 AT3G20410.1 62.637 91 33 1 1 90 349 439 1.69e-29 109
Msa1223310 AT1G50700.3 62.637 91 33 1 1 90 331 421 1.81e-29 109
Msa1223310 AT1G50700.1 62.637 91 33 1 1 90 331 421 2.23e-29 109
Msa1223310 AT1G50700.2 62.637 91 33 1 1 90 331 421 2.65e-29 109
Msa1223310 AT4G21940.1 62.500 88 32 1 4 90 362 449 1.42e-28 107
Msa1223310 AT4G21940.2 62.500 88 32 1 4 90 362 449 1.64e-28 107
Msa1223310 AT4G04720.2 63.636 88 31 1 4 90 340 427 8.04e-28 105
Msa1223310 AT4G04720.1 63.636 88 31 1 4 90 340 427 8.04e-28 105
Msa1223310 AT1G76040.1 61.905 84 31 1 8 90 138 221 1.11e-27 102
Msa1223310 AT1G76040.4 61.905 84 31 1 8 90 138 221 1.11e-27 102
Msa1223310 AT4G21940.3 62.500 88 32 1 4 90 362 449 1.90e-27 103
Msa1223310 AT4G04710.3 62.791 86 31 1 6 90 281 366 5.24e-27 102
Msa1223310 AT1G76040.3 61.905 84 31 1 8 90 376 459 5.91e-27 102
Msa1223310 AT4G04710.2 62.791 86 31 1 6 90 295 380 6.12e-27 102
Msa1223310 AT4G04710.4 62.791 86 31 1 6 90 308 393 6.90e-27 102
Msa1223310 AT4G04710.1 62.791 86 31 1 6 90 308 393 6.98e-27 102
Msa1223310 AT1G76040.2 61.905 84 31 1 8 90 376 459 7.78e-27 102
Msa1223310 AT4G04695.1 59.341 91 35 2 1 90 290 379 2.38e-26 100
Msa1223310 AT1G61950.1 57.955 88 36 1 1 87 357 444 4.67e-26 100
Msa1223310 AT4G23650.1 53.846 91 41 1 1 90 336 426 1.45e-25 98.6
Msa1223310 AT4G04740.2 56.818 88 37 1 4 90 329 416 9.08e-24 93.6
Msa1223310 AT4G04740.4 56.818 88 37 1 4 90 329 416 1.03e-23 93.6
Msa1223310 AT4G04740.6 56.818 88 37 1 4 90 329 416 1.03e-23 93.6
Msa1223310 AT4G04740.5 56.818 88 37 1 4 90 329 416 1.03e-23 93.6
Msa1223310 AT4G04740.3 56.818 88 37 1 4 90 329 416 1.03e-23 93.6
Msa1223310 AT4G04740.1 56.818 88 37 1 4 90 329 416 1.03e-23 93.6
Msa1223310 AT4G04740.7 56.818 88 37 1 4 90 329 416 1.03e-23 93.6
Msa1223310 AT4G04700.1 56.044 91 38 2 1 90 290 379 2.02e-23 92.4
Msa1223310 AT1G35670.1 56.471 85 36 1 7 90 290 374 1.79e-22 90.1
Msa1223310 AT4G09570.1 56.471 85 36 1 7 90 289 373 1.92e-22 89.7
Msa1223310 AT5G12180.1 49.451 91 45 1 1 90 331 421 7.98e-22 88.2
Msa1223310 AT5G04870.1 52.809 89 40 2 3 90 411 498 9.75e-22 88.2
Msa1223310 AT5G19360.1 49.451 91 45 1 1 90 326 416 1.02e-21 87.8
Msa1223310 AT3G10660.2 51.685 89 41 2 3 90 447 534 2.27e-21 87.0
Msa1223310 AT3G10660.1 51.685 89 41 2 3 90 447 534 2.27e-21 87.0
Msa1223310 AT4G38230.1 48.889 90 42 2 5 90 139 228 4.45e-20 82.4
Msa1223310 AT2G17290.1 50.000 90 41 2 5 90 344 433 5.09e-20 83.2
Msa1223310 AT2G17290.2 50.000 90 41 2 5 90 344 433 5.09e-20 83.2
Msa1223310 AT4G35310.2 54.430 79 32 2 5 79 356 434 6.09e-20 82.8
Msa1223310 AT4G35310.1 54.430 79 32 2 5 79 356 434 6.09e-20 82.8
Msa1223310 AT4G38230.4 48.889 90 42 2 5 90 283 372 7.30e-20 82.4
Msa1223310 AT4G38230.3 48.889 90 42 2 5 90 283 372 7.30e-20 82.4
Msa1223310 AT5G23580.1 50.588 85 41 1 7 90 286 370 7.43e-20 82.4
Msa1223310 AT4G38230.2 48.889 90 42 2 5 90 313 402 9.71e-20 82.4
Msa1223310 AT2G38910.1 50.588 85 41 1 7 90 398 482 2.97e-19 80.9
Msa1223310 AT2G35890.2 41.111 90 52 1 1 89 390 479 2.39e-16 72.8
Msa1223310 AT2G35890.1 41.111 90 52 1 1 89 390 479 2.39e-16 72.8
Msa1223310 AT3G51850.3 37.363 91 56 1 1 90 312 402 1.38e-13 64.7
Msa1223310 AT3G51850.2 40.000 85 50 1 7 90 318 402 2.34e-13 64.3
Msa1223310 AT3G51850.1 40.000 85 50 1 7 90 318 402 2.54e-13 63.9
Msa1223310 AT1G18890.1 41.250 80 46 1 1 79 321 400 2.26e-12 61.2
Msa1223310 AT5G19450.2 46.875 64 33 1 16 78 330 393 2.39e-12 61.2
Msa1223310 AT5G19450.1 46.875 64 33 1 16 78 330 393 2.39e-12 61.2
Msa1223310 AT5G12480.2 43.939 66 36 1 16 80 238 303 8.26e-12 59.7
Msa1223310 AT5G12480.1 43.939 66 36 1 16 80 332 397 1.04e-11 59.3
Msa1223310 AT4G36070.2 37.333 75 46 1 1 74 331 405 2.26e-11 58.5
Msa1223310 AT4G36070.1 37.333 75 46 1 1 74 331 405 2.28e-11 58.5
Msa1223310 AT2G31500.1 36.364 77 48 1 1 76 324 400 9.70e-11 56.6

Find 18 sgRNAs with CRISPR-Local

Find 29 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
CAAGGAAACGTTTGAAAATA+TGG 0.208046 8_1:+87768671 Msa1223310:CDS
TATCTAGAATGAAACAATTC+AGG 0.281671 8_1:+87768412 Msa1223310:CDS
AAGACAGGCTTGGCTCGAAT+TGG 0.370556 8_1:+87768732 Msa1223310:CDS
TTAAATACGTTCAAGAAACT+TGG 0.431912 8_1:+87768438 Msa1223310:CDS
CTTCAATTCTTCACAGGTGA+TGG 0.448646 8_1:-87768712 None:intergenic
GTTCAAGAAACTTGGGTTGA+AGG 0.450387 8_1:+87768446 Msa1223310:CDS
TATGGATTTATAACTACTTA+CGG 0.455068 8_1:-87768766 None:intergenic
GCCTGTCTTCAATTCTTCAC+AGG 0.486688 8_1:-87768718 None:intergenic
GGCTGAAAATATAGCGGAAG+AGG 0.497414 8_1:+87768638 Msa1223310:CDS
TAAATACGTTCAAGAAACTT+GGG 0.514172 8_1:+87768439 Msa1223310:CDS
ATCTAGAATGAAACAATTCA+GGG 0.529819 8_1:+87768413 Msa1223310:CDS
TGAAGAATTGAAGACAGGCT+TGG 0.546517 8_1:+87768722 Msa1223310:CDS
ACCTGTGAAGAATTGAAGAC+AGG 0.557454 8_1:+87768717 Msa1223310:CDS
GGAAGAGGTTAAAGATCTCA+AGG 0.583617 8_1:+87768653 Msa1223310:CDS
ATTATCAATCAGTTTATCAG+AGG 0.586571 8_1:-87768382 None:intergenic
GAACACCCGTGGATGAGAGA+CGG 0.635382 8_1:+87768351 None:intergenic
GGTTATGGCTGAAAATATAG+CGG 0.672929 8_1:+87768632 Msa1223310:intron
AATATGGACACTGATCGTAG+TGG 0.763896 8_1:+87768687 Msa1223310:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! ATATATCCAAAAATATAAGC+CGG - chr8_1:87768579-87768598 None:intergenic 20.0%
!! TATGGATTTATAACTACTTA+CGG - chr8_1:87768769-87768788 None:intergenic 20.0%
! ATTATCAATCAGTTTATCAG+AGG - chr8_1:87768385-87768404 None:intergenic 25.0%
!! TATCTAGAATGAAACAATTC+AGG + chr8_1:87768412-87768431 Msa1223310:CDS 25.0%
!! ATCTAGAATGAAACAATTCA+GGG + chr8_1:87768413-87768432 Msa1223310:CDS 25.0%
! TTAAATACGTTCAAGAAACT+TGG + chr8_1:87768438-87768457 Msa1223310:CDS 25.0%
! TAAATACGTTCAAGAAACTT+GGG + chr8_1:87768439-87768458 Msa1223310:CDS 25.0%
!!! ACTTTTTGAGTTACATATAC+CGG + chr8_1:87768557-87768576 Msa1223310:intron 25.0%
! CATTGATTGCTTAGATTAGA+TGG + chr8_1:87768491-87768510 Msa1223310:intron 30.0%
!!! CATATACCGGCTTATATTTT+TGG + chr8_1:87768570-87768589 Msa1223310:intron 30.0%
!! AATTTCCACTAAGTTGGTAA+TGG - chr8_1:87768606-87768625 None:intergenic 30.0%
TAGAGAAATTTCCACTAAGT+TGG - chr8_1:87768612-87768631 None:intergenic 30.0%
AACTTAGTGGAAATTTCTCT+AGG + chr8_1:87768611-87768630 Msa1223310:intron 30.0%
CAAGGAAACGTTTGAAAATA+TGG + chr8_1:87768671-87768690 Msa1223310:CDS 30.0%
TTTCTCCATTACCAACTTAG+TGG + chr8_1:87768598-87768617 Msa1223310:intron 35.0%
GTGGAAATTTCTCTAGGTTA+TGG + chr8_1:87768617-87768636 Msa1223310:intron 35.0%
GGTTATGGCTGAAAATATAG+CGG + chr8_1:87768632-87768651 Msa1223310:intron 35.0%
!! GTTCAAGAAACTTGGGTTGA+AGG + chr8_1:87768446-87768465 Msa1223310:CDS 40.0%
!! AGAAACTTGGGTTGAAGGTA+TGG + chr8_1:87768451-87768470 Msa1223310:intron 40.0%
! TGAAGGTATGGCATGAAACA+TGG + chr8_1:87768463-87768482 Msa1223310:intron 40.0%
! CAGAGTATTCATGCACATGA+TGG - chr8_1:87768536-87768555 None:intergenic 40.0%
GGAAGAGGTTAAAGATCTCA+AGG + chr8_1:87768653-87768672 Msa1223310:CDS 40.0%
AATATGGACACTGATCGTAG+TGG + chr8_1:87768687-87768706 Msa1223310:CDS 40.0%
CTTCAATTCTTCACAGGTGA+TGG - chr8_1:87768715-87768734 None:intergenic 40.0%
ACCTGTGAAGAATTGAAGAC+AGG + chr8_1:87768717-87768736 Msa1223310:CDS 40.0%
TGAAGAATTGAAGACAGGCT+TGG + chr8_1:87768722-87768741 Msa1223310:CDS 40.0%
! GGCTGAAAATATAGCGGAAG+AGG + chr8_1:87768638-87768657 Msa1223310:CDS 45.0%
GCCTGTCTTCAATTCTTCAC+AGG - chr8_1:87768721-87768740 None:intergenic 45.0%
! AAGACAGGCTTGGCTCGAAT+TGG + chr8_1:87768732-87768751 Msa1223310:CDS 50.0%
Chromosome Type Strat End Strand Name
chr8_1 gene 87768363 87768800 87768363 ID=Msa1223310;Name=Msa1223310
chr8_1 mRNA 87768363 87768800 87768363 ID=Msa1223310-mRNA-1;Parent=Msa1223310;Name=Msa1223310-mRNA-1;_AED=0.48;_eAED=0.48;_QI=0|0|0|1|1|1|2|0|90
chr8_1 exon 87768363 87768467 87768363 ID=Msa1223310-mRNA-1:exon:31834;Parent=Msa1223310-mRNA-1
chr8_1 exon 87768633 87768800 87768633 ID=Msa1223310-mRNA-1:exon:31835;Parent=Msa1223310-mRNA-1
chr8_1 CDS 87768363 87768467 87768363 ID=Msa1223310-mRNA-1:cds;Parent=Msa1223310-mRNA-1
chr8_1 CDS 87768633 87768800 87768633 ID=Msa1223310-mRNA-1:cds;Parent=Msa1223310-mRNA-1
Gene Sequence

>Msa1223310

ATGAGAGACGGATGTGAAGCCTCTGATAAACTGATTGATAATGCAGTTCTATCTAGAATGAAACAATTCAGGGCATTAAATACGTTCAAGAAACTTGGGTTGAAGGTTATGGCTGAAAATATAGCGGAAGAGGTTAAAGATCTCAAGGAAACGTTTGAAAATATGGACACTGATCGTAGTGGCACCATCACCTGTGAAGAATTGAAGACAGGCTTGGCTCGAATTGGATCAGAACTGTCCGTAAGTAGTTATAAATCCATAACAAAAGCATGA
Protein sequence

>Msa1223310

MRDGCEASDKLIDNAVLSRMKQFRALNTFKKLGLKVMAENIAEEVKDLKETFENMDTDRSGTITCEELKTGLARIGSELSVSSYKSITKA*